Mercurial > repos > jjohnson > fastqc
comparison fastqc/fastqc.xml @ 0:1d373f219445 default tip
Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
author | jjohnson |
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date | Tue, 07 Jun 2011 17:22:05 -0400 |
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1 <tool id="FastQC" name="FastQC" version="1.0.0"> | |
2 <description>quality control checks on raw sequence data</description> | |
3 <command interpreter="python">fastqc.py | |
4 #if $input.extension.startswith( "fastq"): | |
5 --format=fastq | |
6 #else | |
7 --format=$input.extension | |
8 #end if | |
9 --input='$input' | |
10 --name='$input.name' | |
11 --dir='$report.extra_files_path' | |
12 --report='$report' | |
13 #if $contaminants != None and $contaminants != "None" and $contaminants != "": | |
14 --contaminants=$contaminants | |
15 #end if | |
16 </command> | |
17 <inputs> | |
18 <param name="input" type="data" format="fastq,sam,bam" label="FASTQ reads" /> | |
19 <param name="contaminants" type="data" format="tabular" optional="true" label="Contaminants" | |
20 help="Two fields per line separated by a TAB: name DNA_sequence. For example: Illumina Small RNA RT Primer CAAGCAGAAGACGGCATACGA"/> | |
21 </inputs> | |
22 <outputs> | |
23 <data name="report" format="html" /> | |
24 </outputs> | |
25 <tests> | |
26 <!-- | |
27 <test> | |
28 <param name="input1_file" value="3.fastqsanger" ftype="fastqsanger" /> | |
29 <output name="output1_file" file="split_pair_reads_1.fastqsanger" /> | |
30 <output name="output2_file" file="split_pair_reads_2.fastqsanger" /> | |
31 </test> | |
32 --> | |
33 </tests> | |
34 <help> | |
35 **What it does** | |
36 | |
37 FastQC_ is a product of Bioinformatics Group at the Babraham Institute. FastQC aims to provide a simple way to do some quality control checks on raw sequence data coming from high throughput sequencing pipelines. It provides a modular set of analyses which you can use to give a quick impression of whether your data has any problems of which you should be aware before doing any further analysis. | |
38 | |
39 The main functions of FastQC are:: | |
40 | |
41 - Import of data from BAM, SAM or FastQ files (any variant) | |
42 - Provding a quick overview to tell you in which areas there may be problems | |
43 - Summary graphs and tables to quickly assess your data | |
44 - Export of results to an HTML based permanent report | |
45 - Offline operation to allow automated generation of reports without running the interactive application | |
46 | |
47 | |
48 .. _FastQC: http://www.bioinformatics.bbsrc.ac.uk/projects/fastqc/ | |
49 | |
50 ----- | |
51 | |
52 **Input format** | |
53 | |
54 Any fastq file, for example:: | |
55 | |
56 @HWI-EAS91_1_30788AAXX:7:21:1542:1758 | |
57 GTCAATTGTACTGGTCAATACTAAAAGAATAGGATCGCTCCTAGCATCTGGAGTCTCTATCACCTGAGCCCA | |
58 +HWI-EAS91_1_30788AAXX:7:21:1542:1758 | |
59 hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh`hfhhVZSWehR | |
60 | |
61 **Contaminants format** | |
62 | |
63 An optional contaminant file (otherwise FastQC will use the default):: | |
64 | |
65 # This file contains a list of potential contaminants which are | |
66 # frequently found in high throughput sequencing reactions. These | |
67 # are mostly sequences of adapters / primers used in the various | |
68 # sequencing chemistries. | |
69 # | |
70 # You can add more sequences to the file by putting one line per entry | |
71 # and specifying a name[tab]sequence. If the contaminant you add is | |
72 # likely to be of use to others please consider sending it to the FastQ | |
73 # authors, either via a bug report at www.bioinformatics.bbsrc.ac.uk/bugzilla/ | |
74 # or by directly emailing simon.andrews@bbsrc.ac.uk so other users of | |
75 # the program can benefit. | |
76 Illumina Single End Apapter 1 ACACTCTTTCCCTACACGACGCTGTTCCATCT | |
77 Illumina Single End Apapter 2 CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT | |
78 Illumina Single End PCR Primer 1 AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT | |
79 Illumina Single End PCR Primer 2 CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT | |
80 Illumina Single End Sequencing Primer ACACTCTTTCCCTACACGACGCTCTTCCGATCT | |
81 | |
82 | |
83 ----- | |
84 | |
85 **Outputs** | |
86 | |
87 An HTML file with links to:: | |
88 | |
89 - fastqc_report.html | |
90 - summary.txt | |
91 - fastqc_data.txt | |
92 | |
93 </help> | |
94 </tool> |